Genetic polymorphisms study of pharmacogenomic VIP variants in Han ethnic of China's Shaanxi province

Genetic Polymorphism of Drug Metabolic Gene CYPs, VKORC1, NAT2, DPYD and CHST3 of Five Ethnic Minorities in Heilongjiang Province, Northeast China

Introduction

Genetic variability in genes encoding drug-metabolizing enzymes may contribute to the heterogeneity of drug responses in different populations. Extensive research in pharmacogenomics in major populations around the world provides us with a great deal of information about drug-related genetic polymorphisms.

Objective

The purpose of this study was to detect the genetic variation of drug-metabolism-related genes in the five ethnic minorities Daur, Hezhen, Ewenki, Mongolian and Manchu in China, and to analyze the distribution differences among ethnic groups.

Methods

We genotyped 32 SNPs of drug metabolism genes in 882 healthy Chinese volunteers from five ethnic groups. The genotype frequency and allele frequency of the five ethnic groups were calculated, and the different variants among the five ethnic groups were compared by chi-square test. Genetic parameters were analyzed using Popgene software. The genetic structure of five ethnic minorities was analyzed by principal component analysis, and compared with 26 populations.

Results

We found that SNPs of genes related to drug metabolism existed diversity in different populations. Among them, rs8192766 and rs9419082 in CYP2E1 showed statistical differences between Daur and Manchu, and NAT2 rs1801280 showed statistical differences between Hezhen and Mongolian. In addition, the five populations we studied had the smallest differences with EAS populations. There was haplotype diversity in CHST3, VKORC1, CYP1A2 and CYP2E1 genes in the five ethnic minorities, and these haplotype polymorphisms were related to the use of corresponding drug doses. Cluster analysis shows that the five ethnic minorities in Heilongjiang Province are clustered together with the EAS populations.

Conclusion

These results suggest that understanding the diversity of drug-related genetic markers is critical for individualized drug gene therapy programs in ethnic minorities in China as well as in populations highly mixed with these ethnic groups.

Genetic analysis of pharmacogenomic VIP variants in the Wa population from Yunnan Province of China

Background

The variation of drug responses and target does among individuals is mostly determined by genes. With the development of pharmacogenetics and pharmacogenomics, the differences in drug response between different races seem to be mainly caused by the genetic diversity of pharmacodynamics and pharmacokinetics genes. Very important pharmacogenetic (VIP) variants mean that genes or variants play important and vital roles in drug response, which have been listed in pharmacogenomics databases, such as Pharmacogenomics Knowledge Base (PharmGKB). The information of Chinese ethnic minorities such as the Wa ethnic group is scarce. This study aimed to uncover the significantly different loci in the Wa population in Yunnan Province of China from the perspective of pharmacogenomics, to provide a theoretical basis for the future medication guidance, and to ultimately achieve the best treatment in the future.

Results

In this study, we recruited 200 unrelated healthy Wa adults from the Yunnan province of China, selected 52 VIP variants from the PharmGKB for genotyping. We also compared the genotype frequency and allele distribution of VIP variants between Wa population and the other 26 populations from the 1000 Genomes Project (http://www.1000Genomes.org/). Next, χ² test was used to determine the significant points between these populations. The study results showed that compared with the other 26 population groups, five variants rs776746 (CYP3A5), rs4291 (ACE), rs3093105 (CYP4F2), rs1051298 (SLC19A1), and rs1065852 (CYP2D6) had higher frequencies in the Wa population. The genotype frequencies rs4291-TA, rs3093105-CA, rs1051298-AG and rs1065852-GA were higher than those of the other populations, and the allele distributions of rs4291-T and rs3093105-C were significantly different. Additionally, the difference between the Wa ethnic group and East Asian populations, such as CDX, CHB, and CHS, was the smallest.

Conclusions

Our research results show that there is a significant difference in the distribution of VIP variants between the Wa ethnic group and the other 26 populations. The study results will have an effect on supplementing the pharmacogenomics information for the Wa population and providing a theoretical basis for individualised medication for the Wa population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-00999-8.

Population Genetic Difference of Pharmacogenomic VIP Variants in the Tibetan Population

Background

Genetic variation influences drug reaction or adverse prognosis. The purpose of this research was to genotype very important pharmacogenetic (VIP) variants in the Tibetan population.

Methods and Materials

Blood samples from 200 Tibetans were randomly collected and 59 VIP variants were genotyped, and then compared our data to 26 other populations in the 1000 project to further analyze and identify significant difference.

Results

The results showed that on comparing with most of the 26 populations from the 1000 project, rs4291 (ACE), rs1051296 (SLC19A1) and rs1065852 (CYP2D6) significantly differed in the Tibetan population. Furthermore, three significant loci were related to drug response. In addition, the allele frequency of Tibetans least differed from that of East Asian populations, and most differed from that of Americans.

Conclusion

Three significant loci of variation ACE rs4291, SLC19A1 rs1051296 and CYP2D6 rs1065852 were associated with drug response. This result will contribute to improving the information of the Tibetan in the pharmacogenomics database, and providing a theoretical basis for clinical individualised drug use in Tibetans.

Genetic variation of pharmacogenomic VIP variants in Zhuang nationality of southern China

Drug gene polymorphisms are strongly associated with disease. Previous studies have shown that the frequency of drug genes varies in different populations. At present, there are no reports about the polymorphism of the drug genome in the Zhuang population in southern China. This study conducted a pharmacogenomics study on the Zhuang population in southern China. Therefore, we conducted genotyping on 105 Zhuang samples, and compared the genotyping results with those of other 11 ethnic groups after statistical analysis. Our results show that, compared with the 11 populations in the HapMap data set, the differences between the CYP2E1 rs2070676 and CYP2D6 rs1065852 of the Zhuang nationality are the largest. This study fills in the blank of the drug genome information of the Zhuang nationality in southern China. The two sites of Rs2070676 (CYP2E1) and rs1065852 (CYP2D6) provide a reliable basis for the prediction of the efficacy of certain drugs. Its main purpose is to provide theoretical basis for safe drug use in the Zhuang region of southern China.

Genetic polymorphisms of pharmacogenomic VIP variants in the Dai population from Yunnan province

Background

Pharmacogenomics plays a crucial role in individualized therapy, but the variant information of pharmacogenomics in the Dai population is limited. We therefore aimed to screen very important pharmacogenetic (VIP) in the Dai population and compared differences between Dai and other 25 populations.

Methods

In this study, we genotyped 73 VIP variants from the PharmGKB and compared genotype distribution of variants in Dai with other 25 populations by χ2 test. To assess the genetic relationship among 26 populations, we performed the structure analysis. In addition, pair‐wise F‐statistics (Fst) was calculated to measure the population differentiation.

Results

We found 12, 10, 13, 17, 11, 39, 46, 46, 45, 43, 49, 46, 46, 46, 49, 45, 41, 42, 48, 53, 45, 50, 50, 51, 47, and 50 significantly different variants in Dai compared with other 25 populations. Genetic structure analysis showed Dai had close relationships with CDX (Chinese Dai in Xishuangbanna), CHB (Han Chinese in Beijing), JPT (Japanese in Tokyo), and KHV (Kinh in Ho Chi Minh City, Vietnam). Moreover, Dai is the most similar to KHV according to Fst analysis.

Conclusions

Our study complement the pharmacogenomics information of Dai population from Yunnan province and provide a theoretical basis for personalized medicine.

Genetic polymorphisms analysis of pharmacogenomic VIP variants in Bai ethnic group from China

Background

The pharmacogenomics study has been widely used for the study of very important pharmacogenetic (VIP) variants among different ethnic groups. However, there is little known about the pharmacogenomics information regarding Bai family. Our study aimed to screen the polymorphism of the VIP gene in Bai nationality.

Methods

We genotyped 81 VIP variants (selected from the PharmGKB database) in the Bai population and then compared them to the other 11 major HapMap populations by chi‐square test, structure and F‐statistics (Fst) analysis.

Results

Our results indicated that rs20417 (PTGS2), rs4148323 (UGT1A), and rs1131596 (SLC19A1) were most different in Bai compared with most of the 11 populations from the HapMap data set. Furthermore, population structure and F‐statistics (Fst) analysis also demonstrated that the Bai population has the closest genetic relationship with Han Chinese in Beijing, China (CHB), followed by Japanese in Tokyo, Japan (JPT), and the farthest population from the Yoruba in Ibadan, Nigeria (YRI).

Conclusions

Our study not only presented the genotype frequency difference between the selected population of the Bai population and the other 11 populations, but also showed that the Bai population is most similar to the CHB populations, followed by JPT. These findings would contribute to the development of individualized medicine for the Bai population.

Genetic polymorphisms of pharmacogenomic VIP variants in the Lisu population of southwestern China: A cohort study

Pharmacogenomic studies of different ethnic or racial groups have been used to develop personalized therapies specific to subjects. This study aimed to identify the distribution differences of very important pharmacogenetic (VIP) variants between the Lisu population from southwestern China and other ethnic groups.Eighty VIP variants in 37 genes were selected from the pharmacogenomic knowledge base (PharmGKB), and compared with genotype data of the Lisu population then compared with other 11 populations from the HapMap dataset and previously published data including Miao, Li, Deng, Sherpa, Lhoba, Tibetan, Kirghiz, Tajik, Mongol, Shaanxi Han ethnic, and Uygur populations.VDR rs1540339, MTHFR rs1801131, P2RY1 rs701265, and PTGS2 rs689466 were significantly different between Lisu and 11 HapMap populations. ANKK1 rs1800497 was the least statistical significant locus among selected single nucleotide polymorphisms. In addition, genetic background of Lisu was strongly closest to Shaanxi Han ethnic cohort, and followed by Chinese in metropolitan Denver population based on population structure and F-statistics analyses.Our results showed significant interethnic differences between Lisu and other populations, which will give useful information for prospective studies and better individualized treatments.

Genetic polymorphisms in very important pharmacogenomic variants in the Zhuang ethnic group of Southwestern China: A cohort study in the Zhuang population

Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations.We genotyped 80 variants of VIP genes in 100 unrelated healthy Zhuang adults from the Yunnan province of China. Next, we analyzed the genotyping data with Structure and F-statistics (Fst).We compared our data with those of other populations using the HapMap data set, and observed that the frequency distribution of Zhuang population in Yunnan closely resembles that of JPT. Furthermore, population structure and Fst analysis showed that the Zhuang population is closely related to the Shaanxi Han population with respect to genetic background.Our study supplements existing information on Zhuang population pharmacogenomics and provides an extensive overview for developing personalized medicine.